diff --git a/bwamem.c b/bwamem.c
index eb24e67..fc34fca 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -537,7 +537,20 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
 			w = max_gap < opt->w? max_gap : opt->w;
 			if (qd - rd < w && rd - qd < w) break;
 		}
-		if (i < av->n) continue;
+		if (i < av->n) { // the seed is (almost) contained in an existing alignment
+			for (i = k + 1; i < c->n; ++i) { // check overlapping seeds in the same chain
+				const mem_seed_t *t;
+				if (srt[i] == 0) continue;
+				t = &c->seeds[(uint32_t)srt[i]];
+				if (t->len < s->len * .95) continue; // only check overlapping if t is long enough; TODO: more efficient by early stopping
+				if (s->qbeg <= t->qbeg && s->qbeg + s->len >= t->qbeg && t->qbeg - s->qbeg != t->rbeg - s->rbeg) break;
+				if (t->qbeg <= s->qbeg && t->qbeg + t->len >= s->qbeg && s->qbeg - t->qbeg != s->rbeg - t->rbeg) break;
+			}
+			if (i == c->n) { // no overlapping seeds; then skip extension
+				srt[k] = 0; // mark that seed extension has not been performed
+				continue;
+			}
+		}
 
 		a = kv_pushp(mem_alnreg_t, *av);
 		memset(a, 0, sizeof(mem_alnreg_t));
@@ -555,7 +568,7 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
 			for (i = 0; i < MAX_BAND_TRY; ++i) {
 				int prev = a->score;
 				aw[0] = opt->w << i;
-				a->score = ksw_extend(s->qbeg, qs, tmp, rs, 5, opt->mat, opt->q, opt->r, aw[0], opt->zdrop, s->len * opt->a, &qle, &tle, &gtle, &gscore, &max_off[0]);
+				a->score = ksw_extend(s->qbeg, qs, tmp, rs, 5, opt->mat, opt->q, opt->r, aw[0], opt->pen_clip, opt->zdrop, s->len * opt->a, &qle, &tle, &gtle, &gscore, &max_off[0]);
 				if (bwa_verbose >= 4) { printf("L\t%d < %d; w=%d; max_off=%d\n", prev, a->score, aw[0], max_off[0]); fflush(stdout); }
 				if (a->score == prev || max_off[0] < (aw[0]>>1) + (aw[0]>>2)) break;
 			}
@@ -578,7 +591,7 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
 			for (i = 0; i < MAX_BAND_TRY; ++i) {
 				int prev = a->score;
 				aw[1] = opt->w << i;
-				a->score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, aw[1], opt->zdrop, sc0, &qle, &tle, &gtle, &gscore, &max_off[1]);
+				a->score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, aw[1], opt->pen_clip, opt->zdrop, sc0, &qle, &tle, &gtle, &gscore, &max_off[1]);
 				if (bwa_verbose >= 4) { printf("R\t%d < %d; w=%d; max_off=%d\n", prev, a->score, aw[1], max_off[1]); fflush(stdout); }
 				if (a->score == prev || max_off[1] < (aw[1]>>1) + (aw[1]>>2)) break;
 			}
@@ -863,6 +876,13 @@ mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *
 	a.NM = NM;
 	pos = bns_depos(bns, rb < bns->l_pac? rb : re - 1, &is_rev);
 	a.is_rev = is_rev;
+	if (a.n_cigar > 0) {
+		if ((a.cigar[0]&0xf) == 2) {
+			pos += a.cigar[0]>>4;
+			--a.n_cigar;
+			memmove(a.cigar, a.cigar + 1, a.n_cigar * 4);
+		} else if ((a.cigar[a.n_cigar-1]&0xf) == 2) --a.n_cigar;
+	}
 	if (qb != 0 || qe != l_query) { // add clipping to CIGAR
 		int clip5, clip3;
 		clip5 = is_rev? l_query - qe : qb;
diff --git a/bwamem.h b/bwamem.h
index b7a4e79..40f47f8 100644
--- a/bwamem.h
+++ b/bwamem.h
@@ -16,6 +16,7 @@ typedef struct __smem_i smem_i;
 #define MEM_F_NOPAIRING 0x4
 #define MEM_F_ALL       0x8
 #define MEM_F_NO_MULTI  0x10
+#define MEM_F_NO_RESCUE 0x20
 
 typedef struct {
 	int a, b, q, r;         // match score, mismatch penalty and gap open/extension penalty. A gap of size k costs q+k*r
diff --git a/bwamem_pair.c b/bwamem_pair.c
index 8329ebe..19fc83b 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -235,20 +235,21 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 
 	int n = 0, i, j, z[2], o, subo, n_sub, extra_flag = 1;
 	kstring_t str;
-	mem_alnreg_v b[2];
 	mem_aln_t h[2];
 
 	str.l = str.m = 0; str.s = 0;
-	// perform SW for the best alignment
-	kv_init(b[0]); kv_init(b[1]);
-	for (i = 0; i < 2; ++i)
-		for (j = 0; j < a[i].n; ++j)
-			if (a[i].a[j].score >= a[i].a[0].score  - opt->pen_unpaired)
-				kv_push(mem_alnreg_t, b[i], a[i].a[j]);
-	for (i = 0; i < 2; ++i)
-		for (j = 0; j < b[i].n && j < opt->max_matesw; ++j)
-			n += mem_matesw(opt, bns->l_pac, pac, pes, &b[i].a[j], s[!i].l_seq, (uint8_t*)s[!i].seq, &a[!i]);
-	free(b[0].a); free(b[1].a);
+	if (!(opt->flag & MEM_F_NO_RESCUE)) { // then perform SW for the best alignment
+		mem_alnreg_v b[2];
+		kv_init(b[0]); kv_init(b[1]);
+		for (i = 0; i < 2; ++i)
+			for (j = 0; j < a[i].n; ++j)
+				if (a[i].a[j].score >= a[i].a[0].score  - opt->pen_unpaired)
+					kv_push(mem_alnreg_t, b[i], a[i].a[j]);
+		for (i = 0; i < 2; ++i)
+			for (j = 0; j < b[i].n && j < opt->max_matesw; ++j)
+				n += mem_matesw(opt, bns->l_pac, pac, pes, &b[i].a[j], s[!i].l_seq, (uint8_t*)s[!i].seq, &a[!i]);
+		free(b[0].a); free(b[1].a);
+	}
 	mem_mark_primary_se(opt, a[0].n, a[0].a);
 	mem_mark_primary_se(opt, a[1].n, a[1].a);
 	if (opt->flag&MEM_F_NOPAIRING) goto no_pairing;
@@ -305,7 +306,7 @@ no_pairing:
 			h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[0]);
 		else h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, 0);
 	}
-	if (h[0].rid == h[1].rid && h[0].rid >= 0) { // if the top hits from the two ends constitute a proper pair, flag it.
+	if (!(opt->flag & MEM_F_NOPAIRING) && h[0].rid == h[1].rid && h[0].rid >= 0) { // if the top hits from the two ends constitute a proper pair, flag it.
 		int64_t dist;
 		int d;
 		d = mem_infer_dir(bns->l_pac, a[0].a[0].rb, a[1].a[0].rb, &dist);
diff --git a/bwase.c b/bwase.c
index 718dd5d..85efcbd 100644
--- a/bwase.c
+++ b/bwase.c
@@ -176,7 +176,7 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
 		rseq = bns_get_seq(l_pac, pacseq, rb, re, &rlen);
 		seq_reverse(len, seq, 0); // as we need to do left extension, we have to reverse both query and reference sequences
 		seq_reverse(rlen, rseq, 0);
-		ksw_extend(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, -1, len<<1, &qle, &tle, &gtle, &gscore, 0);
+		ksw_extend(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, 0, -1, len<<1, &qle, &tle, &gtle, &gscore, 0);
 		if (gscore > 0) tle = gtle, qle = len;
 		rb = re - tle; rlen = tle;
 		seq_reverse(len, seq, 0);
@@ -192,7 +192,7 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
 		rb = *_pos; re = rb + len + SW_BW;
 		if (re > l_pac) re = l_pac;
 		rseq = bns_get_seq(l_pac, pacseq, rb, re, &rlen);
-		ksw_extend(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, -1, len<<1, &qle, &tle, &gtle, &gscore, 0);
+		ksw_extend(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, 0, -1, len<<1, &qle, &tle, &gtle, &gscore, 0);
 		if (gscore > 0) tle = gtle, qle = len;
 		re = rb + tle; rlen = tle;
 		ksw_global(qle, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, n_cigar, &cigar32); // right extension
diff --git a/bwt.c b/bwt.c
index 412dce5..edd0afc 100644
--- a/bwt.c
+++ b/bwt.c
@@ -370,6 +370,18 @@ void bwt_dump_sa(const char *fn, const bwt_t *bwt)
 	err_fclose(fp);
 }
 
+static bwtint_t fread_fix(FILE *fp, bwtint_t size, void *a)
+{ // Mac/Darwin has a bug when reading data longer than 2GB. This function fixes this issue by reading data in small chunks
+	const int bufsize = 0x1000000; // 16M block
+	bwtint_t offset = 0;
+	while (size) {
+		int x = bufsize < size? bufsize : size;
+		if ((x = err_fread_noeof(a + offset, 1, x, fp)) == 0) break;
+		size -= x; offset += x;
+	}
+	return offset;
+}
+
 void bwt_restore_sa(const char *fn, bwt_t *bwt)
 {
 	char skipped[256];
@@ -388,7 +400,7 @@ void bwt_restore_sa(const char *fn, bwt_t *bwt)
 	bwt->sa = (bwtint_t*)xcalloc(bwt->n_sa, sizeof(bwtint_t));
 	bwt->sa[0] = -1;
 
-	err_fread_noeof(bwt->sa + 1, sizeof(bwtint_t), bwt->n_sa - 1, fp);
+	fread_fix(fp, sizeof(bwtint_t) * (bwt->n_sa - 1), bwt->sa + 1);
 	err_fclose(fp);
 }
 
@@ -405,7 +417,7 @@ bwt_t *bwt_restore_bwt(const char *fn)
 	err_fseek(fp, 0, SEEK_SET);
 	err_fread_noeof(&bwt->primary, sizeof(bwtint_t), 1, fp);
 	err_fread_noeof(bwt->L2+1, sizeof(bwtint_t), 4, fp);
-	err_fread_noeof(bwt->bwt, 4, bwt->bwt_size, fp);
+	fread_fix(fp, bwt->bwt_size<<2, bwt->bwt);
 	bwt->seq_len = bwt->L2[4];
 	err_fclose(fp);
 	bwt_gen_cnt_table(bwt);
diff --git a/bwtsw2_aux.c b/bwtsw2_aux.c
index 88c13c7..074af10 100644
--- a/bwtsw2_aux.c
+++ b/bwtsw2_aux.c
@@ -125,7 +125,7 @@ void bsw2_extend_left(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *_query, int lq
 		for (k = p->k - 1, j = 0; k > 0 && j < lt; --k) // FIXME: k=0 not considered!
 			target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
 		lt = j;
-		score = ksw_extend(p->beg, &query[lq - p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, -1, p->G, &qle, &tle, 0, 0, 0);
+		score = ksw_extend(p->beg, &query[lq - p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, 0, -1, p->G, &qle, &tle, 0, 0, 0);
 		if (score > p->G) { // extensible
 			p->G = score;
 			p->k -= tle;
@@ -153,7 +153,7 @@ void bsw2_extend_rght(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *query, int lq,
 		for (k = p->k, j = 0; k < p->k + lt && k < l_pac; ++k)
 			target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
 		lt = j;
-		score = ksw_extend(lq - p->beg, &query[p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, -1, 1, &qle, &tle, 0, 0, 0) - 1;
+		score = ksw_extend(lq - p->beg, &query[p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, 0, -1, 1, &qle, &tle, 0, 0, 0) - 1;
 //		if (score < p->G) fprintf(stderr, "[bsw2_extend_hits] %d < %d\n", score, p->G);
 		if (score >= p->G) {
 			p->G = score;
diff --git a/fastmap.c b/fastmap.c
index 76e3c03..7ff73cb 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -27,7 +27,7 @@ int main_mem(int argc, char *argv[])
 	void *ko = 0, *ko2 = 0;
 
 	opt = mem_opt_init();
-	while ((c = getopt(argc, argv, "paMCPHk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:")) >= 0) {
+	while ((c = getopt(argc, argv, "paMCSPHk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:")) >= 0) {
 		if (c == 'k') opt->min_seed_len = atoi(optarg);
 		else if (c == 'w') opt->w = atoi(optarg);
 		else if (c == 'A') opt->a = atoi(optarg);
@@ -43,6 +43,7 @@ int main_mem(int argc, char *argv[])
 		else if (c == 'a') opt->flag |= MEM_F_ALL;
 		else if (c == 'p') opt->flag |= MEM_F_PE;
 		else if (c == 'M') opt->flag |= MEM_F_NO_MULTI;
+		else if (c == 'S') opt->flag |= MEM_F_NO_RESCUE;
 		else if (c == 'c') opt->max_occ = atoi(optarg);
 		else if (c == 'd') opt->zdrop = atoi(optarg);
 		else if (c == 'v') bwa_verbose = atoi(optarg);
@@ -64,7 +65,8 @@ int main_mem(int argc, char *argv[])
 		fprintf(stderr, "       -r FLOAT   look for internal seeds inside a seed longer than {-k} * FLOAT [%g]\n", opt->split_factor);
 //		fprintf(stderr, "       -s INT     look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width);
 		fprintf(stderr, "       -c INT     skip seeds with more than INT occurrences [%d]\n", opt->max_occ);
-		fprintf(stderr, "       -P         skip pairing; perform mate SW only\n");
+		fprintf(stderr, "       -S         skip mate rescue\n");
+		fprintf(stderr, "       -P         skip pairing; mate rescue performed unless -S also in use\n");
 		fprintf(stderr, "       -A INT     score for a sequence match [%d]\n", opt->a);
 		fprintf(stderr, "       -B INT     penalty for a mismatch [%d]\n", opt->b);
 		fprintf(stderr, "       -O INT     gap open penalty [%d]\n", opt->q);
diff --git a/ksw.c b/ksw.c
index 700afd0..f5b24dc 100644
--- a/ksw.c
+++ b/ksw.c
@@ -360,7 +360,7 @@ typedef struct {
 	int32_t h, e;
 } eh_t;
 
-int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off)
+int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off)
 {
 	eh_t *eh; // score array
 	int8_t *qp; // query profile
@@ -382,7 +382,7 @@ int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
 	k = m * m;
 	for (i = 0, max = 0; i < k; ++i) // get the max score
 		max = max > mat[i]? max : mat[i];
-	max_gap = (int)((double)(qlen * max - gapo) / gape + 1.);
+	max_gap = (int)((double)(qlen * max + end_bonus - gapo) / gape + 1.);
 	max_gap = max_gap > 1? max_gap : 1;
 	w = w < max_gap? w : max_gap;
 	// DP loop
diff --git a/ksw.h b/ksw.h
index 2dd6499..97559fd 100644
--- a/ksw.h
+++ b/ksw.h
@@ -102,7 +102,7 @@ extern "C" {
 	 *
 	 * @return        best semi-local alignment score
 	 */
-	int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int zdrop, int h0, int *qle, int *tle, int *gtle, int *gscore, int *max_off);
+	int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int end_bonus, int zdrop, int h0, int *qle, int *tle, int *gtle, int *gscore, int *max_off);
 
 #ifdef __cplusplus
 }
diff --git a/main.c b/main.c
index ca110a7..b1aa9cf 100644
--- a/main.c
+++ b/main.c
@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.3-r369-beta"
+#define PACKAGE_VERSION "0.7.3-r375-beta"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);